Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment.

Koalas (Phascolarctos cinereus) are arboreal marsupials native to Australia that eat a specialized diet of almost exclusively eucalyptus leaves. Microbes in koala intestines are known to break down otherwise toxic compounds, such as tannins, in eucalyptus leaves. Infections by Chlamydia, obligate intracellular bacterial pathogens, are highly prevalent in koala populations. If animals with Chlamydia infections are received by wildlife hospitals, a range of antibiotics can be used to treat them. However, previous studies suggested that koalas can suffer adverse side effects during antibiotic treatment. This study aimed to use 16S rRNA gene sequences derived from koala feces to characterize the intestinal microbiome of koalas throughout antibiotic treatment and identify specific taxa associated with koala health after treatment. Although differences in the alpha diversity were observed in the intestinal flora between treated and untreated koalas and between koalas treated with different antibiotics, these differences were not statistically significant. The alpha diversity of microbial communities from koalas that lived through antibiotic treatment versus those who did not was significantly greater, however. Beta diversity analysis largely confirmed the latter observation, revealing that the overall communities were different between koalas on antibiotics that died versus those that survived or never received antibiotics. Using both machine learning and OTU (operational taxonomic unit) co-occurrence network analyses, we found that OTUs that are very closely related to Lonepinella koalarum, a known tannin degrader found by culture-based methods to be present in koala intestines, was correlated with a koala's health status. This is the first study to characterize the time course of effects of antibiotics on koala intestinal microbiomes. Our results suggest it may be useful to pursue alternative treatments for Chlamydia infections without the use of antibiotics or the development of Chlamydia-specific antimicrobial compounds that do not broadly affect microbial communities

Koala Poop Smells Good: How I Know This and Ways to Increase the Impact of Research Through Education & Outreach

Koalas (Phascolarctos cinereus) are arboreal marsupials native to Australia that subsist on a diet almost exclusively of Eucalyptus leaves. Eucalyptus leaves contain many toxic compounds, yet koalas are able to tolerate this toxic diet with strategies independent and dependent of their intestinal microbial communities. Koala populations across Australia have a high prevalence of Chlamydia infections. Wild koalas are often brought into wildlife hospitals to be tested and treated for Chlamydia infections, but there is evidence that these antibiotic treatments can cause severe negative side effects in koalas. Chapter 1 explores how the intestinal bacterial communities of koalas shift throughout antibiotic treatment and identifies taxa that are strongly correlated with koala survival during treatment. The most predictive taxa of a koala surviving antibiotic treatment was identified as Lonepinella koalarum, a bacteria known to degrade tannins, a common toxin found in Eucalyptus leaves. While this finding suggests that L. koalarum may be important for koala health, it is unclear what role this bacteria plays in degrading toxins found in Eucalyptus leaves. To provide insight for this, Chapter 2 describes the whole genome sequencing of L. koalarum as well as several analyses of the genome assembly aimed at determining potential toxin degradation functionality. The second part of the dissertation discusses some of the ways in which the content covered in Chapter 1 and Chapter 2 was used for education and outreach. For example, the research was funded in part by a successful crowdfunding campaign (Chapter 3), the generation of isolates from koala feces was used as the curriculum for a Course Based Undergraduate Research Experience (Chapter 4), and the importance of L. koalarum was used to teach young audiences about the symbiotic relationships (Chapter 5). These examples highlight how research can be used for education and outreach, which engages an audience far outside the realms of academia. Chapter 6 is yet another example of how current research can be rewritten to reach young audiences. The best way way to engage learners in science (or otherwise) is to utilize teaching techniques for active learning. It has been known for centuries that students learn significantly better when they are actively learning, but lecture-based teaching practices are still profolific, especially in higher education. In Chapter 7, I argue that teaching for active learning does not have to be cost or time prohibitive; the chapter outlines non-time-consuming and cost-free teaching strategies for all audiences

Koala Project Sequence Raw Data

Raw 16s sequencing data from koala fecal materia

Crowdfunding Campaigns Help Researchers Launch Projects and Generate Outreach

Organizers of participatory research (citizen science) projects can generate funds and outreach through crowdfunding. Here we provide insights from three successful science crowdfunding campaigns recently completed on Indiegogo, Experiment, and Kickstarter. Choosing a crowdfunding platform that fits the project is just the beginning; a successful campaign reflects its content, management, and marketing, and some researchers may need to acquire new skills. In addition, the growing trend of crowdfunding for science reinforces the importance of academic engagement with social media

Crowdfunding Campaigns Help Researchers Launch Projects and Generate Outreach

Organizers of participatory research (citizen science) projects can generate funds and outreach through crowdfunding. Here we provide insights from three successful science crowdfunding campaigns recently completed on Indiegogo, Experiment, and Kickstarter. Choosing a crowdfunding platform that fits the project is just the beginning; a successful campaign reflects its content, management, and marketing, and some researchers may need to acquire new skills. In addition, the growing trend of crowdfunding for science reinforces the importance of academic engagement with social media

Best Practices for Microbiome Study Design in Companion Animal Research.

The gut microbiome is a community of microorganisms that inhabits an animal host's gastrointestinal tract, with important effects on animal health that are shaped by multiple environmental, dietary, and host-associated factors. Clinical and dietary trials in companion animals are increasingly including assessment of the microbiome, but interpretation of these results is often hampered by suboptimal choices in study design. Here, we review best practices for conducting feeding trials or clinical trials that intend to study the effects of an intervention on the microbiota. Choices for experimental design, including a review of basic designs, controls, and comparison groups, are discussed in the context of special considerations necessary for microbiome studies. Diet is one of the strongest influences on the composition of gut microbiota, so applications specific to nutritional interventions are discussed in detail. Lastly, we provide specific advice for successful recruitment of colony animals and household pets into an intervention study. This review is intended to serve as a resource to academic and industry researchers, clinicians, and veterinarians alike, for studies that test many different types of interventions

Best Practices for Microbiome Study Design in Companion Animal Research.

The gut microbiome is a community of microorganisms that inhabits an animal host's gastrointestinal tract, with important effects on animal health that are shaped by multiple environmental, dietary, and host-associated factors. Clinical and dietary trials in companion animals are increasingly including assessment of the microbiome, but interpretation of these results is often hampered by suboptimal choices in study design. Here, we review best practices for conducting feeding trials or clinical trials that intend to study the effects of an intervention on the microbiota. Choices for experimental design, including a review of basic designs, controls, and comparison groups, are discussed in the context of special considerations necessary for microbiome studies. Diet is one of the strongest influences on the composition of gut microbiota, so applications specific to nutritional interventions are discussed in detail. Lastly, we provide specific advice for successful recruitment of colony animals and household pets into an intervention study. This review is intended to serve as a resource to academic and industry researchers, clinicians, and veterinarians alike, for studies that test many different types of interventions